ArticleBioinformatics (Oxford, England)2010
Efficient genome ancestry inference in complex pedigrees with inbreeding.
Article in Bioinformatics (Oxford, England), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- MalKinID: A classification model for identifying malaria parasite genealogical relationships using identity-by-descent.Genetics · 2025Article
- MalKinID: A Likelihood-Based Model for Identifying Malaria Parasite Genealogical Relationships Using Identity-by-Descent.bioRxiv : the preprint server for biology · 2024Article
- Reliable genotyping of recombinant genomes using a robust hidden Markov model.Plant physiology · 2023Article
- SPEARS: Standard Performance Evaluation of Ancestral haplotype Reconstruction through Simulation.Bioinformatics (Oxford, England) · 2021Article
- Ancestral haplotype reconstruction in endogamous populations using identity-by-descent.PLoS computational biology · 2021Article
- Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding.Heredity · 2020Review
- Determinants of QTL Mapping Power in the Realized Collaborative Cross.G3 (Bethesda, Md.) · 2019Article
- Recursive Algorithms for Modeling Genomic Ancestral Origins in a Fixed Pedigree.G3 (Bethesda, Md.) · 2018Article
- Inbred Strain Variant Database (ISVdb): A Repository for Probabilistically Informed Sequence Differences Among the Collaborative Cross Strains and Their Founders.G3 (Bethesda, Md.) · 2017Article
- Male Infertility Is Responsible for Nearly Half of the Extinction Observed in the Mouse Collaborative Cross.Genetics · 2017Article
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- Plethysmography Phenotype QTL in Mice Before and After Allergen Sensitization and Challenge.G3 (Bethesda, Md.) · 2016Article
- R2d2 Drives Selfish Sweeps in the House Mouse.Molecular biology and evolution · 2016Article
- Article
- Informatics resources for the Collaborative Cross and related mouse populations.Mammalian genome : official journal of the International Mammalian Genome Society · 2015Review
- Identification of microRNAs associated with allergic airway disease using a genetically diverse mouse population.BMC genomics · 2015Article
- Article
- Modeling X-linked ancestral origins in multiparental populations.G3 (Bethesda, Md.) · 2015Article
- A multi-megabase copy number gain causes maternal transmission ratio distortion on mouse chromosome 2.PLoS genetics · 2015Article
- Article
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5 authors.
Funding
Abstract
motivationHigh-density SNP data of model animal resources provides opportunities for fine-resolution genetic variation studies. These genetic resources are generated through a variety of breeding schemes that involve multiple generations of matings derived from a set of founder animals. In this article, we investigate the problem of inferring the most probable ancestry of resulting genotypes, given a set of founder genotypes. Due to computational difficulty, existing methods either handle only small pedigree data or disregard the pedigree structure. However, large pedigrees of model animal resources often contain repetitive substructures that can be utilized in accelerating computation.
resultsWe present an accurate and efficient method that can accept complex pedigrees with inbreeding in inferring genome ancestry. Inbreeding is a commonly used process in generating genetically diverse and reproducible animals. It is often carried out for many generations and can account for most of the computational complexity in real-world model animal pedigrees. Our method builds a hidden Markov model that derives the ancestry probabilities through inbreeding process without explicit modeling in every generation. The ancestry inference is accurate and fast, independent of the number of generations, for model animal resources such as the Collaborative Cross (CC). Experiments on both simulated and real CC data demonstrate that our method offers comparable accuracy to those methods that build an explicit model of the entire pedigree, but much better scalability with respect to the pedigree size.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.